Chrome Portable setting separate from desktop version

I have Chrome installed locally on my PC, but I also installed it to my thumb drive for use elsewhere when needed. I got it all setup with my Google account, so it pulled in all my extensions, tabs, startup pages and such. My question though is this, is there a way to make the portable version not open up all the startup pages upon loading that the desktop version does. Since the setting are all tied together, I know that if delete all the starup pages from one, it'll sync to the other copy and delete them from that as well.

I know that I could just use the one copy on the thumbdrive, but there's always the chance of loosing access to the thumb drive for whatever reason(theft, loss, damage, etc), so I prefer to keep and use the locally installed one and just use the portable one when I'm away from my PC.